## [1] "Wed Jan 31 13:11:39 2024"

1 LOINC codes for chemical tests (class = “CHEM”)

## [1] "LOINC codes for chemical tests: loinc_data/loinc_chem_names.tsv"
## [1] "LOINC codes: 10606"

2 NextMove LeadMine NER output using GeneAndProtein dictionary.

NER = named entity recognition, a form of text-mining.

2.1 NER on LOINC field: “component”.

## [1] "NextMove NER for LOINC-component: loinc_data/loinc_chem_names_2_NM_CFDictGeneAndProtein_leadmine.tsv"
## [1] "LOINC codes mapped via component text to NER proteins: 1878"
## [1] "LOINC codes resolved to standard IDs: 990 / 1878"
## [1] "LOINC codes resolved to HGNC IDs: 809 / 1878"
## [1] "LOINC codes resolved to UniProt IDs: 50 / 1878"
## [1] "LOINC codes resolved to Entrez (gene?) IDs: 132 / 1878"

2.2 NER on LOINC field: “relatednames2”.

How many added by this field?

## [1] "NextMove NER for LOINC-relatednames: loinc_data/loinc_chem_names_6_NM_CFDictGeneAndProtein_leadmine.tsv"
## [1] "LOINC codes mapped via relatednames2 text to NER proteins: 1874"
## [1] "LOINC codes mapped via relatednames2 AND mapped via component: 1263"
## [1] "LOINC codes mapped via relatednames2 NOT mapped via component: 611"
## [1] "LOINC codes resolved to standard IDs: 1239 / 1874"

3 Cerner RWD counts

Cerner Real World Data 2023 counts of distinct encounter_ids and patient_ids for LOINC codes of class “CHEM”. Each count is for a specific lab test, and year. Some different labs have same LOINC codes, i.e. some Cerner-coded lab tests merge to the same LOINC code. Also, the counts cannot be added, since there may be common patients and encounters.

## [1] "LOINC codes in RWD encounters: 3593"
## [1] "Number of labs tests which merge to a common LOINC, in representative year 2021: 9 / 2981"

3.1 Group lab procedures into list; aggregate on LOINC codes.

3.2 Combine years for totals.

Encounter ID counts can be added for multiple years, but not patient ID counts, since there can be common ID. When added over multiple labs, encounter ID counts should be interpreted as lab counts, since a single encounter can involve multiple labs.

## [1] "Total LOINCs: 3593; total lab-encounters: 8e+10"

4 LOINC proteins in RWD encounters

## [1] "LOINC codes for proteins in RWD encounters: 868"
## [1] "LOINC protein names in RWD encounters: 421"

4.1 Group protein synonyms into list; aggregate on LOINC codes.

5 Top occurring LOINCs

For now, remove data without resolved protein IDs. And the few Ensembl IDs, pending clarification on ENSG vs ENSP.

Top occurring LOINCs (top 50 / 515, with 122 unique gene-protein IDs)
loinc_code geneOrProteinId mnemonics lab_count
1751-7 HGNC:399 Albumin [Mass/volume] in Serum or Plasma 99530276
1742-6 HGNC:4552 Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma 99448917
1759-0 HGNC:399 Albumin/Globulin [Mass Ratio] in Serum or Plasma 47030076
1968-7 HGNC:399 Bilirubin.direct [Mass/volume] in Serum or Plasma 39076770
3040-3 HGNC:6619 Lipase [Enzymatic activity/volume] in Serum or Plasma 36872904
1743-4 HGNC:4552 Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma by With P-5’-P 15184942
61152-5 HGNC:399 Albumin [Mass/volume] in Serum or Plasma by Bromocresol purple (BCP) dye binding method 11031598
1744-2 HGNC:4552 Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma by No addition of P-5’-P 10648619
2857-1 UNIPROT:P07288 Prostate specific Ag [Mass/volume] in Serum or Plasma 9823612
61151-7 HGNC:399 Albumin [Mass/volume] in Serum or Plasma by Bromocresol green (BCG) dye binding method 9233502
2276-4 UNIPROT:Q26061 Ferritin [Mass/volume] in Serum or Plasma 8445047
14957-5 HGNC:399 Microalbumin [Mass/volume] in Urine 6172810
2502-3 HGNC:11740 Iron saturation [Mass Fraction] in Serum or Plasma 5600674
14959-1 HGNC:399 Microalbumin/Creatinine [Mass Ratio] in Urine 4458248
2731-8 HGNC:9606 Parathyrin.intact [Mass/volume] in Serum or Plasma 3020605
14338-8 HGNC:399 Prealbumin [Mass/volume] in Serum or Plasma 2754876
2324-2 UNIPROT:P63186 Gamma glutamyl transferase [Enzymatic activity/volume] in Serum or Plasma 2406028
3034-6 HGNC:11740 Transferrin [Mass/volume] in Serum or Plasma 2160471
1754-1 HGNC:399 Albumin [Mass/volume] in Urine 2077739
1747-5 HGNC:399 Albumin [Mass/volume] in Body fluid 1764137
2874-6 UNIPROT:Q65479 Gamma globulin [Mass/volume] in Serum or Plasma by Electrophoresis 1405639
9318-7 HGNC:399 Albumin/Creatinine [Mass Ratio] in Urine 1365878
1916-6 HGNC:4552 Aspartate aminotransferase/Alanine aminotransferase [Enzymatic activity ratio] in Serum or Plasma 1286362
2862-1 HGNC:399 Albumin [Mass/volume] in Serum or Plasma by Electrophoresis 1283018
44429-9 HGNC:399 Albumin/Globulin [Mass Ratio] in Serum or Plasma by Electrophoresis 1280969
10501-5 UNIPROT:P01231 Lutropin [Units/volume] in Serum or Plasma 1076989
2842-3 HGNC:9445 Prolactin [Mass/volume] in Serum or Plasma 1059015
46099-8 HGNC:399 Calcium [Mass/volume] corrected for albumin in Serum or Plasma 988146
2639-3 HGNC:6915 Myoglobin [Mass/volume] in Serum or Plasma 987685
1834-1 HGNC:317 Alpha-1-Fetoprotein [Mass/volume] in Serum or Plasma 774174
20448-7 HGNC:6081 Insulin [Units/volume] in Serum or Plasma 703189
1825-9 UNIPROT:P22922 Alpha 1 antitrypsin [Mass/volume] in Serum or Plasma 699936
13967-5 HGNC:10839 Sex hormone binding globulin [Moles/volume] in Serum or Plasma 624428
76625-3 HGNC:4552 Alanine aminotransferase [Enzymatic activity/volume] in Blood 619940
50949-7 HGNC:399 Albumin [Presence] in Urine by Test strip 615220
10886-0 UNIPROT:P07288 Prostate Specific Ag Free [Mass/volume] in Serum or Plasma 509922
6875-9 UNIPROT:P15941 Cancer Ag 15-3 [Units/volume] in Serum or Plasma 493760
20567-4 UNIPROT:Q26061 Ferritin [Mass/volume] in Serum or Plasma by Immunoassay 478926
53962-7 HGNC:317 Alpha-1-fetoprotein.tumor marker [Mass/volume] in Serum or Plasma 459542
46761-3 HGNC:1122 Biotinidase deficiency newborn screen interpretation 452287
12841-3 UNIPROT:P07288 Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma 429179
2742-5 HGNC:2707 Angiotensin converting enzyme [Enzymatic activity/volume] in Serum or Plasma 420194
33358-3 UNIPROT:P54296 Protein.monoclonal [Mass/volume] in Serum or Plasma by Electrophoresis 420043
15061-5 HGNC:3415 Erythropoietin (EPO) [Units/volume] in Serum or Plasma 410958
17842-6 UNIPROT:Q02496 Cancer Ag 27-29 [Units/volume] in Serum or Plasma 393225
32769-2 UNIPROT:P22922 Alpha 1 antitrypsin phenotype [Interpretation] in Serum or Plasma; Alpha 1 antitrypsin phenotyping [Interpretation] in Serum or Plasma 382692
32769-2 UNIPROT:P22922 Alpha 1 antitrypsin phenotyping [Interpretation] in Serum or Plasma; Alpha 1 antitrypsin phenotype [Interpretation] in Serum or Plasma 382692
32769-2 UNIPROT:P22922 Alpha 1 antitrypsin phenotype [Interpretation] in Serum or Plasma 382692
2484-4 HGNC:5464 Insulin-like growth factor-I [Mass/volume] in Serum or Plasma 345762
3013-0 HGNC:11764 Thyroglobulin [Mass/volume] in Serum or Plasma 317568